I cam on an F1 visa in 2009 and 2010 onwards started my OPT. My OPT expired in 2011 and I went on a J 1 visa as a research scholar after being 2 student years on F1 F1 OPT. Can I claim the India -US treaty for FICA exemption and any other tax exemption for the next 2 years of my visa starting now?

You can only be exempt from counting days for the substantial presence test, if you haven't already been exempt 2 out of the last 6 years (the 6-year look back rule). Since you were exempt on your F1 visa in 2009 and 2010, you cannot be exempt on J1.